Java Code Examples for org.hl7.fhir.dstu3.model.ElementDefinition#setPath()

private void produceProperties(List<ElementDefinition> elements, String name, List<Property> properties, boolean attrMode, boolean snapshot) throws FHIRFormatError {
  for (Property p : properties) {
    if (p.isattr == attrMode) {
      ElementDefinition ed = new ElementDefinition();
      elements.add(ed);
      ed.setPath(name+"."+p.name);
      if (p.type.startsWith("xsd:"))
        ToolingExtensions.addStringExtension(ed.addType(), ToolingExtensions.EXT_XML_TYPE, p.type);
      else
        ed.addType().setCode(p.type);
      ed.setMin(p.min);
      ed.setMax(p.max == Integer.MAX_VALUE ? "*" : Integer.toString(p.max));
      ed.setDefinition(p.doco);
      if (p.isattr)
        ed.addRepresentation(PropertyRepresentation.XMLATTR);
      if (p.binding != null)
        ed.getBinding().setStrength(BindingStrength.REQUIRED).setValueSet(new UriType("http://hl7.org/fhir/iso21090/ValueSet/"+p.binding));
      if (snapshot)
        ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
    }
  }
}
 

private void genElements(StructureDefinition sd, String path, NodeTreeEntry item) throws Exception {
  ElementDefinition ed = sd.getSnapshot().addElement();
  ed.setPath(path);
  ed.setMax(item.cardinality.max);
  ed.setMin(Integer.parseInt(item.cardinality.min));
  ed.setShort(texts.get(item.atCode).text);
  ed.setDefinition(texts.get(item.atCode).description);
  ed.setComment(texts.get(item.atCode).comment);
  Element te = findTypeElement(item.typeName);
  if (te.hasAttribute("profile"))
    ed.addType().setCode(te.getAttribute("fhir")).setProfile(te.getAttribute("profile"));
  else
  	ed.addType().setCode(te.getAttribute("fhir"));
   ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());

 	for (NodeTreeEntry child : item.children) {
 		genElements(sd, path+"."+child.name, child);
 	}
}
 

private void closeChildren(StructureDefinition base, ElementDefinition edb, StructureDefinition derived, ElementDefinition edm) {
  String path = edb.getPath()+".";
  int baseStart = base.getSnapshot().getElement().indexOf(edb);
  int baseEnd = findEnd(base.getSnapshot().getElement(), edb, baseStart+1);
  int diffStart = derived.getDifferential().getElement().indexOf(edm);
  int diffEnd = findEnd(derived.getDifferential().getElement(), edm, diffStart+1);
  
  for (int cBase = baseStart; cBase < baseEnd; cBase++) {
    ElementDefinition edBase = base.getSnapshot().getElement().get(cBase);
    if (isImmediateChild(edBase, edb)) {
      ElementDefinition edMatch = getMatchInDerived(edBase, derived.getDifferential().getElement(), diffStart, diffEnd);
      if (edMatch == null) {
        ElementDefinition edd = derived.getDifferential().addElement();
        edd.setPath(edBase.getPath());
        edd.setMax("0");
      } else {
        closeChildren(base, edBase, derived, edMatch);
      }        
    }
  }
}
 

private void testSlicingTask8742() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Organization.address");
  id.setMin(1);
  id.setMax("1");
  id.setMustSupport(true);
      
  id = focus.getDifferential().addElement();
  id.setPath("Organization.address.extension");
  id.setSliceName("USLabCountycodes");
  id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("url").setType(DiscriminatorType.VALUE);
  id.setShort("County/Parish FIPS codes");
  id.setDefinition("County/Parish FIPS codes.");
  id.setRequirements("County/Parish Code SHALL use FIPS 6-4  ( INCITS 31:2009).");
  id.setMin(0);
  id.setMax("1");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/us-core-county");
  id.setMustSupport(true);
  id.getBinding().setStrength(BindingStrength.REQUIRED).setDescription("FIPS codes for US counties and county equivalent entities.").setValueSet(new Reference().setReference("http://hl7.org/fhir/ValueSet/fips-county"));
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 14 for address with one sliced extension
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 13;
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation test 8742 failed");
  } else 
    System.out.println("Snap shot generation test 8742 passed");
}
 

private void generateType(DataType dt) throws Exception {
  StructureDefinition sd = new StructureDefinition();
  sd.setId(dt.name);
  sd.setUrl("http://hl7.org/fhir/iso21090/StructureDefinition/"+sd.getId());
  sd.setName(dt.name+" data type");
  sd.setStatus(PublicationStatus.ACTIVE);
  sd.setExperimental(false);
  sd.setPublisher("HL7 / ISO");
  sd.setDate(new Date());
  sd.setDescription(dt.doco);
  sd.setKind(StructureDefinitionKind.LOGICAL);
  sd.setAbstract(Utilities.existsInList(dt.name, "HXIT", "QTY"));
  sd.setType("Element");
  if (dt.parent == null)
    sd.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Element");
  else
    sd.setBaseDefinition("http://hl7.org/fhir/iso21090/StructureDefinition/"+dt.parent);
  sd.setDerivation(TypeDerivationRule.SPECIALIZATION);
  ElementDefinition ed = sd.getDifferential().addElement();
  ed.setPath(dt.name);
  produceProperties(sd.getDifferential().getElement(), dt.name, dt.properties, true, false);
  produceProperties(sd.getDifferential().getElement(), dt.name, dt.properties, false, false);
  ed = sd.getSnapshot().addElement();
  ed.setPath(dt.name);
  if (dt.parent != null)
    addParentProperties(sd.getSnapshot().getElement(), dt.name, dt.parent, true, true);
  produceProperties(sd.getSnapshot().getElement(), dt.name, dt.properties, true, true);
  if (dt.parent != null)
    addParentProperties(sd.getSnapshot().getElement(), dt.name, dt.parent, false, true);
  produceProperties(sd.getSnapshot().getElement(), dt.name, dt.properties, false, true);
  ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
  new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("c:\\temp\\iso21090\\StructureDefinition-"+dt.name+".xml"), sd);    
}
 

/**
 * Change one cardinality.
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testCardinalityChange() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setMin(1);
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMin() == 1;
          if (ok)
            f.setMin(0);
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation chenge cardinality test failed");
  } else 
    System.out.println("Snap shot generation chenge cardinality test passed");
}
 

private void copyElements(StructureDefinition sd, List<ElementDefinition> list) {
  for (ElementDefinition ed : list) {
    if (ed.getPath().contains(".")) {
      ElementDefinition n = ed.copy();
      n.setPath(sd.getSnapshot().getElementFirstRep().getPath()+"."+ed.getPath().substring(ed.getPath().indexOf(".")+1));
      sd.getSnapshot().addElement(n);
    }
  }
}
 

public void closeDifferential(StructureDefinition base, StructureDefinition derived) throws FHIRException {
  for (ElementDefinition edb : base.getSnapshot().getElement()) {
    if (isImmediateChild(edb) && !edb.getPath().endsWith(".id")) {
      ElementDefinition edm = getMatchInDerived(edb, derived.getDifferential().getElement());
      if (edm == null) {
        ElementDefinition edd = derived.getDifferential().addElement();
        edd.setPath(edb.getPath());
        edd.setMax("0");
      } else if (edb.hasSlicing()) {
        closeChildren(base, edb, derived, edm);
      }
    }
  }
  sortDifferential(base, derived, derived.getName(), new ArrayList<String>());
}
 

/**
   * left and right refer to the same element. Are they compatible?   
   * @param outcome 
   * @param outcome
   * @param path
   * @param left
   * @param right
   * @- if there's a problem that needs fixing in this code
   * @throws DefinitionException 
   * @throws IOException 
   * @throws FHIRFormatError 
   */
  private boolean compareElements(ProfileComparison outcome, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
//    preconditions:
    assert(path != null);
    assert(left != null);
    assert(right != null);
    assert(left.path().equals(right.path()));
    
    // we ignore slicing right now - we're going to clone the root one anyway, and then think about clones 
    // simple stuff
    ElementDefinition subset = new ElementDefinition();
    subset.setPath(left.path());
    
    // not allowed to be different: 
    subset.getRepresentation().addAll(left.current().getRepresentation()); // can't be bothered even testing this one
    if (!outcome.ruleCompares(subset, left.current().getDefaultValue(), right.current().getDefaultValue(), path+".defaultValue[x]", BOTH_NULL))
      return false;
    subset.setDefaultValue(left.current().getDefaultValue());
    if (!outcome.ruleEqual(path, subset, left.current().getMeaningWhenMissing(), right.current().getMeaningWhenMissing(), "meaningWhenMissing Must be the same", true))
      return false;
    subset.setMeaningWhenMissing(left.current().getMeaningWhenMissing());
    if (!outcome.ruleEqual(subset, left.current().getIsModifier(), right.current().getIsModifier(), path, "isModifier"))
      return false;
    subset.setIsModifier(left.current().getIsModifier());
    if (!outcome.ruleEqual(subset, left.current().getIsSummary(), right.current().getIsSummary(), path, "isSummary"))
      return false;
    subset.setIsSummary(left.current().getIsSummary());
    
    // descriptive properties from ElementDefinition - merge them:
    subset.setLabel(mergeText(subset, outcome, path, "label", left.current().getLabel(), right.current().getLabel()));
    subset.setShort(mergeText(subset, outcome, path, "short", left.current().getShort(), right.current().getShort()));
    subset.setDefinition(mergeText(subset, outcome, path, "definition", left.current().getDefinition(), right.current().getDefinition()));
    subset.setComment(mergeText(subset, outcome, path, "comments", left.current().getComment(), right.current().getComment()));
    subset.setRequirements(mergeText(subset, outcome, path, "requirements", left.current().getRequirements(), right.current().getRequirements()));
    subset.getCode().addAll(mergeCodings(left.current().getCode(), right.current().getCode()));
    subset.getAlias().addAll(mergeStrings(left.current().getAlias(), right.current().getAlias()));
    subset.getMapping().addAll(mergeMappings(left.current().getMapping(), right.current().getMapping()));
    // left will win for example
    subset.setExample(left.current().hasExample() ? left.current().getExample() : right.current().getExample());

    subset.setMustSupport(left.current().getMustSupport() || right.current().getMustSupport());
    ElementDefinition superset = subset.copy();


    // compare and intersect
    superset.setMin(unionMin(left.current().getMin(), right.current().getMin()));
    superset.setMax(unionMax(left.current().getMax(), right.current().getMax()));
    subset.setMin(intersectMin(left.current().getMin(), right.current().getMin()));
    subset.setMax(intersectMax(left.current().getMax(), right.current().getMax()));
    outcome.rule(subset, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
    
    superset.getType().addAll(unionTypes(path, left.current().getType(), right.current().getType()));
    subset.getType().addAll(intersectTypes(subset, outcome, path, left.current().getType(), right.current().getType()));
    outcome.rule(subset, !subset.getType().isEmpty() || (!left.current().hasType() && !right.current().hasType()), path, "Type Mismatch:\r\n  "+typeCode(left)+"\r\n  "+typeCode(right));
//    <fixed[x]><!-- ?? 0..1 * Value must be exactly this --></fixed[x]>
//    <pattern[x]><!-- ?? 0..1 * Value must have at least these property values --></pattern[x]>
    superset.setMaxLengthElement(unionMaxLength(left.current().getMaxLength(), right.current().getMaxLength()));
    subset.setMaxLengthElement(intersectMaxLength(left.current().getMaxLength(), right.current().getMaxLength()));
    if (left.current().hasBinding() || right.current().hasBinding()) {
      compareBindings(outcome, subset, superset, path, left.current(), right.current());
    }

    // note these are backwards
    superset.getConstraint().addAll(intersectConstraints(path, left.current().getConstraint(), right.current().getConstraint()));
    subset.getConstraint().addAll(unionConstraints(subset, outcome, path, left.current().getConstraint(), right.current().getConstraint()));

    // now process the slices
    if (left.current().hasSlicing() || right.current().hasSlicing()) {
      if (isExtension(left.path()))
        return compareExtensions(outcome, path, superset, subset, left, right);
//      return true;
      else
        throw new DefinitionException("Slicing is not handled yet");
    // todo: name 
    }

    // add the children
    outcome.subset.getSnapshot().getElement().add(subset);
    outcome.superset.getSnapshot().getElement().add(superset);
    return compareChildren(subset, outcome, path, left, right);
  }
 

private PropertyWithType updateProfile(VariableForProfiling var, String element, TypeDetails type, StructureMap map, List<StructureDefinition> profiles, String sliceName, Type fixed, StructureMapGroupRuleTargetComponent tgt) throws FHIRException {
    if (var == null) {
      assert (Utilities.noString(element));
      // 1. start the new structure definition
      StructureDefinition sdn = worker.fetchResource(StructureDefinition.class, type.getType());
      if (sdn == null)
        throw new FHIRException("Unable to find definition for "+type.getType());
      ElementDefinition edn = sdn.getSnapshot().getElementFirstRep();
      PropertyWithType pn = createProfile(map, profiles, new PropertyWithType(sdn.getId(), new Property(worker, edn, sdn), null, type), sliceName, tgt);

//      // 2. hook it into the base bundle
//      if (type.getType().startsWith("http://hl7.org/fhir/StructureDefinition/") && worker.getResourceNames().contains(type.getType().substring(40))) {
//        StructureDefinition sd = var.getProperty().profileProperty.getStructure();
//        ElementDefinition ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry");
//        ed.setName(sliceName);
//        ed.setMax("1"); // well, it is for now...
//        ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry.fullUrl");
//        ed.setMin(1);
//        ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry.resource");
//        ed.setMin(1);
//        ed.addType().setCode(pn.getProfileProperty().getStructure().getType()).setProfile(pn.getProfileProperty().getStructure().getUrl());
//      }
      return pn; 
    } else {
      assert (!Utilities.noString(element));
      Property pvb = var.getProperty().getBaseProperty();
      Property pvd = var.getProperty().getProfileProperty();
      Property pc = pvb.getChild(element, var.property.types);
      if (pc == null)
        throw new DefinitionException("Unable to find a definition for "+pvb.getDefinition().getPath()+"."+element);
      
      // the profile structure definition (derived)
      StructureDefinition sd = var.getProperty().profileProperty.getStructure();
      ElementDefinition ednew = sd.getDifferential().addElement();
      ednew.setPath(var.getProperty().profileProperty.getDefinition().getPath()+"."+pc.getName());
      ednew.setUserData("slice-name", sliceName);
      ednew.setFixed(fixed);
      for (ProfiledType pt : type.getProfiledTypes()) {
        if (pt.hasBindings())
          ednew.setBinding(pt.getBindings().get(0));
        if (pt.getUri().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
          String t = pt.getUri().substring(40);
          t = checkType(t, pc, pt.getProfiles());
          if (t != null) {
            if (pt.hasProfiles()) {
              for (String p : pt.getProfiles())
                if (t.equals("Reference"))
                  ednew.addType().setCode(t).setTargetProfile(p);
                else
                  ednew.addType().setCode(t).setProfile(p);
            } else 
            ednew.addType().setCode(t);
      }
        }
      }
      
      return new PropertyWithType(var.property.path+"."+element, pc, new Property(worker, ednew, sd), type);
    }
  }
 

private PropertyWithType createProfile(StructureMap map, List<StructureDefinition> profiles, PropertyWithType prop, String sliceName, Base ctxt) throws DefinitionException {
  if (prop.getBaseProperty().getDefinition().getPath().contains(".")) 
    throw new DefinitionException("Unable to process entry point");

  String type = prop.getBaseProperty().getDefinition().getPath();
  String suffix = "";
  if (ids.containsKey(type)) {
    int id = ids.get(type);
    id++;
    ids.put(type, id);
    suffix = "-"+Integer.toString(id);
  } else
    ids.put(type, 0);
  
  StructureDefinition profile = new StructureDefinition();
  profiles.add(profile);
  profile.setDerivation(TypeDerivationRule.CONSTRAINT);
  profile.setType(type);
  profile.setBaseDefinition(prop.getBaseProperty().getStructure().getUrl());
  profile.setName("Profile for "+profile.getType()+" for "+sliceName);
  profile.setUrl(map.getUrl().replace("StructureMap", "StructureDefinition")+"-"+profile.getType()+suffix);
  ctxt.setUserData("profile", profile.getUrl()); // then we can easily assign this profile url for validation later when we actually transform
  profile.setId(map.getId()+"-"+profile.getType()+suffix);
  profile.setStatus(map.getStatus());
  profile.setExperimental(map.getExperimental());
  profile.setDescription("Generated automatically from the mapping by the Java Reference Implementation");
  for (ContactDetail c : map.getContact()) {
    ContactDetail p = profile.addContact();
    p.setName(c.getName());
    for (ContactPoint cc : c.getTelecom()) 
      p.addTelecom(cc);
  }
  profile.setDate(map.getDate());
  profile.setCopyright(map.getCopyright());
  profile.setFhirVersion(Constants.VERSION);
  profile.setKind(prop.getBaseProperty().getStructure().getKind());
  profile.setAbstract(false);
  ElementDefinition ed = profile.getDifferential().addElement();
  ed.setPath(profile.getType());
  prop.profileProperty = new Property(worker, ed, profile);
  return prop;
}
 

/**
 * check that documentation appending is working
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testDocumentationAppend() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setDefinition("... some more doco");
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getDefinition().length() > b.getDefinition().length();
          if (ok) {
            f.setDefinition(null);
            b.setDefinition(null);
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation documentation append failed");
  } else 
    System.out.println("Snap shot generation documentation append test passed");
}
 

/**
 * check that narrowing types is working
 * this one doesn't rename the path
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void textTypeNarrowing1() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.deceased[x]");
  id.addType().setCode("dateTime");
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.deceasedDateTime")) {
          ok = f.getType().size() == 1 && f.getType().get(0).getCode().equals("dateTime");
          if (ok) {
            f.getType().clear();
            b.getType().clear();
            f.setPath(b.getPath());
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation narrow type 1 failed");
  } else 
    System.out.println("Snap shot generation narrow type 1 test passed");
}
 

/**
 * check that narrowing types is working
 * this one renames the path
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void textTypeNarrowing2() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.deceasedDateTime");
  id.addType().setCode("dateTime");
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.deceasedDateTime")) {
          ok = f.getType().size() == 1 && f.getType().get(0).getCode().equals("dateTime");
          if (ok) {
            f.getType().clear();
            b.getType().clear();
            f.setPath(b.getPath());
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation narrow type 2 failed");
  } else 
    System.out.println("Snap shot generation narrow type 2 test passed");
}
 

/**
 * check that mapping resolution is working
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testMapping() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.addMapping().setIdentity("rim").setMap("test");
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMapping().size() > b.getMapping().size();
          if (ok) {
            f.getMapping().clear();
            b.getMapping().clear();
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation mapping changes failed");
  } else 
    System.out.println("Snap shot generation mapping changes test passed");
}
 

/**
 * Walking into a type 
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testTypeWalk() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setMustSupport(true);
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.system");
  id.setMustSupport(true);
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // the derived should be 8 longer
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 8;
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i <= 9 ? i : i + 8);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMustSupport() && !b.getMustSupport();
          if (ok) {
            f.setMustSupportElement(null);
          }
        }
        ok = Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation simple test failed");
  } else 
    System.out.println("Snap shot generation simple test passed");
}
 

/**
 * Walking into a type, without explicitly doing so 
 * 
 * note: this currently fails.
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testTypeWalk2() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.system");
  id.setMustSupport(true);
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // the derived should be 8 longer
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 8;
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i <= 9 ? i : i + 8);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMustSupport() && !b.getMustSupport();
          if (ok) {
            f.setMustSupportElement(null);
          }
        }
        ok = Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation simple test failed");
  } else 
    System.out.println("Snap shot generation simple test passed");
}
 

/**
 * we're going to slice Patient.identifier
 */
private void testSlicingSimple() throws EOperationOutcome, Exception {
  
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  
  // set the slice up
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("use").setType(DiscriminatorType.VALUE);
  
  // first slice: 
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setSliceName("name1");
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.use");
  id.setFixed(new CodeType("usual"));
  
  // second slice:
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setSliceName("name2");
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.use");
  id.setFixed(new CodeType("official"));
  
  
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 18 different: identifier + 8 inner children * 2 
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 18;
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i <= 9 ? i : i + 18);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.hasSlicing();
          if (ok)
            f.setSlicing(null);
        }            
        ok = Base.compareDeep(b, f, true);
      }
    }
  }
  // now, check that the slices we skipped are correct:
  for (int i = 10; i <= 18; i++) {
    if (ok) {
      ElementDefinition d1 = focus.getSnapshot().getElement().get(i);
      ElementDefinition d2 = focus.getSnapshot().getElement().get(i+9);
      if (d1.getPath().equals("Patient.identifier.use")) {
        ok = d1.hasFixed() && d2.hasFixed() && !Base.compareDeep(d1.getFixed(), d2.getFixed(), true);
        if (ok) {
          d1.setFixed(null);
          d2.setFixed(null);
        }
      }
      if (d1.getPath().equals("Patient.identifier")) {
        ok = d1.hasSliceName() && d2.hasSliceName() && !Base.compareDeep(d1.getSliceNameElement(), d2.getSliceNameElement(), true);
        if (ok) {
          d1.setSliceName(null);
          d2.setSliceName(null);
        }
      }
      ok = Base.compareDeep(d1, d2, true);
    }
  }
  // for throughness, we could check against identifier too, but this is not done now.
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation slicing failed");
  } else 
    System.out.println("Snap shot generation slicing passed");
  
}
 

/**
 * we're going to slice Patient.extension and refer to extension by profile
 * 
 * implicit: whether to rely on implicit extension slicing
 */
private void testSlicingExtension(boolean implicit) throws EOperationOutcome, Exception {
  
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  
  // set the slice up
  ElementDefinition id;
  if (!implicit) {
    id = focus.getDifferential().addElement();
    id.setPath("Patient.extension");
    id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("url").setType(DiscriminatorType.VALUE);
    id.setMax("3");
  }
  // first slice: 
  id = focus.getDifferential().addElement();
  id.setPath("Patient.extension");
  id.setSliceName("name1");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/patient-birthTime");
  id.setMin(1);
  
  // second slice:
  id = focus.getDifferential().addElement();
  id.setPath("Patient.extension");
  id.setSliceName("name2");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");    
  
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  ProfileUtilities pu = new ProfileUtilities(context, messages, null);
  pu.generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 2 different: extension slices 
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 2;
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i <= 7 ? i : i + 2);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.extension")) {
          ok = f.hasSlicing() && (implicit || f.getMax().equals("3"));
          if (ok) {
            f.setSlicing(null);
            f.setMaxElement(b.getMaxElement());
          }
        }            
        if (!f.getPath().equals("Patient.extension")) // no compare that because the definitions get overwritten 
          ok = Base.compareDeep(b, f, true);
      }
    }
  }
  // now, check that the slices we skipped are correct:
  if (ok) {
    ElementDefinition d1 = focus.getSnapshot().getElement().get(8);
    ElementDefinition d2 = focus.getSnapshot().getElement().get(9);
    ok = d1.hasType() && d1.getType().get(0).hasProfile() && d2.hasType() && d2.getType().get(0).hasProfile() && !Base.compareDeep(d1.getType(), d2.getType(), true) &&
          d1.getMin() == 1 && d2.getMin() == 0 && d1.getMax().equals("1") && d2.getMax().equals("1");
    if (ok) {
      d1.getType().clear();
      d2.getType().clear();
      d1.setSliceName("x");
      d2.setSliceName("x");
      d1.setMin(0);
    }
    ok = Base.compareDeep(d1, d2, true);
    // for throughness, we could check against extension too, but this is not done now.
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation slicing extensions simple ("+(implicit ? "implicit" : "not implicit")+") failed");
  } else 
    System.out.println("Snap shot generation slicing extensions simple ("+(implicit ? "implicit" : "not implicit")+") passed");
}